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fix skip bugs

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This commit is contained in:
nw13slx
2021-12-11 16:41:13 -05:00
parent 250a5921a3
commit 8f99d8d1d9
4 changed files with 78 additions and 51 deletions
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4
src/reader_native.cpp
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@ -174,7 +174,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
return 1;
}
match_field(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
match_fields(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
return natoms;
}
@ -186,7 +186,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
xyz flag set by scaleflag + wrapflag (if fieldlabel set) or column label
------------------------------------------------------------------------- */
void ReaderNative::match_field(int nfield,
void ReaderNative::match_fields(int nfield,
int &xflag, int &yflag, int &zflag,
int *fieldtype, char **fieldlabel,
int scaleflag, int wrapflag, int &fieldflag,

4
src/reader_native.h
View File

@ -41,8 +41,8 @@ class ReaderNative : public Reader {
protected:
int *fieldindex; //
void match_field(int, int &, int &, int &, int *, char **, int, int, int &,
std::map<std::string, int>);
void match_fields(int, int &, int &, int &, int *, char **, int, int, int &,
std::map<std::string, int>);
private:
char *line; // line read from dump file

118
src/reader_native_bin.cpp
View File

@ -20,6 +20,7 @@
#include <cstring>
#include <utility>
#include <iostream>
using namespace LAMMPS_NS;
@ -31,12 +32,14 @@ enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
ReaderNativeBin::ReaderNativeBin(LAMMPS *lmp) : ReaderNative(lmp)
{
fieldindex = nullptr;
buf = new double[maxbuf];
}
/* ---------------------------------------------------------------------- */
ReaderNativeBin::~ReaderNativeBin()
{
delete [] buf;
memory->destroy(fieldindex);
}
@ -89,38 +92,54 @@ int ReaderNativeBin::read_time(bigint &ntimestep)
void ReaderNativeBin::skip()
{
bigint natoms;
int triclinic;
skip_buf(sizeof(bigint));
read_buf(&triclinic, sizeof(int), 1);
skip_buf((sizeof(int)+sizeof(double))*6);
if (triclinic) {
skip_buf(sizeof(double)*3);
}
skip_buf(sizeof(int));
skip_reading_magic_str();
// read chunk and skip them
int nchunk;
read_buf(&nchunk, sizeof(int), 1);
if (feof(fp)) {
error->one(FLERR,"Unexpected end of dump file");
}
double *buf = new double[maxbuf];
int n;
for (int i = 0; i < nchunk; i++) {
int n;
read_buf(&n, sizeof(int), 1);
// extend buffer to fit chunk size
if (n > maxbuf) {
if (buf) delete[] buf;
buf = new double[n];
maxbuf = n;
}
// read chunk and write as size_one values per line
read_buf(buf, sizeof(double), n);
if (feof(fp)) {
error->one(FLERR,"Unexpected end of dump file");
}
read_double_chunk(n);
}
delete[] buf;
delete[] magic_string;
delete[] unit_style;
magic_string = nullptr;
unit_style = nullptr;
}
void ReaderNativeBin::skip_reading_magic_str()
{
if (magic_string && revision > 0x0001) {
int len;
read_buf(&len, sizeof(int), 1);
if (len > 0) {
// has units
skip_buf(sizeof(char)*len);
}
char flag = 0;
read_buf(&flag, sizeof(char), 1);
if (flag) {
skip_buf(sizeof(double));
}
read_buf(&len, sizeof(int), 1);
skip_buf(sizeof(char)*len);
}
}
/* ----------------------------------------------------------------------
@ -154,24 +173,24 @@ bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclin
int boundary[3][2];
read_buf(&triclinic, sizeof(int), 1);
read_buf(&boundary[0][0], 6 * sizeof(int), 1);
read_buf(&box[0][0], sizeof(double), 1);
read_buf(&box[0][1], sizeof(double), 1);
read_buf(&box[1][0], sizeof(double), 1);
read_buf(&box[1][1], sizeof(double), 1);
read_buf(&box[2][0], sizeof(double), 1);
read_buf(&box[2][1], sizeof(double), 1);
read_buf(&boundary[0][0], sizeof(int), 6);
read_buf(box[0], sizeof(double), 2);
read_buf(box[1], sizeof(double), 2);
read_buf(box[2], sizeof(double), 2);
if (triclinic) {
read_buf(&box[0][2], sizeof(double), 1);
read_buf(&box[1][2], sizeof(double), 1);
read_buf(&box[2][2], sizeof(double), 1);
}
if (!fieldinfo) return natoms;
// exatract column labels and match to requested fields
read_buf(&size_one, sizeof(int), 1);
if (!fieldinfo) {
skip_reading_magic_str();
return natoms;
}
int len = 0;
char *labelline;
@ -214,7 +233,8 @@ bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclin
return 1;
}
match_field(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
match_fields(nfield, xflag, yflag, zflag, fieldtype, fieldlabel, scaleflag, wrapflag, fieldflag, labels);
return natoms;
}
@ -232,7 +252,6 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
error->one(FLERR,"Unexpected end of dump file");
}
double *buf = new double[maxbuf];
int i_atom = 0;
int nchunk;
read_buf(&nchunk, sizeof(int), 1);
@ -240,17 +259,8 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
read_buf(&n, sizeof(int), 1);
// extend buffer to fit chunk size
if (n > maxbuf) {
if (buf) delete[] buf;
buf = new double[n];
maxbuf = n;
}
// read chunk and write as size_one values per line
read_buf(buf, sizeof(double), n);
read_double_chunk(n);
n /= size_one;
int m = 0;
for (int j = 0; j < n; j++)
@ -263,11 +273,8 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
}
}
delete[] buf;
delete[] magic_string;
delete[] unit_style;
magic_string = nullptr;
unit_style = nullptr;
}
void ReaderNativeBin::read_buf(void * ptr, size_t size, size_t count)
@ -276,4 +283,21 @@ void ReaderNativeBin::read_buf(void * ptr, size_t size, size_t count)
// detect end-of-file
if (feof(fp)) error->one(FLERR,"Unexpected end of dump file");
}
void ReaderNativeBin::read_double_chunk(size_t count)
{
// extend buffer to fit chunk size
if (count > maxbuf) {
if (buf) delete[] buf;
buf = new double[count];
maxbuf = count;
}
read_buf(buf, sizeof(double), count);
}
void ReaderNativeBin::skip_buf(size_t size)
{
char tmp[size];
read_buf(tmp, 1, size);
}

3
src/reader_native_bin.h
View File

@ -48,6 +48,9 @@ class ReaderNativeBin : public ReaderNative {
double *buf;
void read_buf(void *, size_t, size_t);
void read_double_chunk(size_t);
void skip_buf(size_t);
void skip_reading_magic_str();
};
} // namespace LAMMPS_NS